[2024-01-24 10:57:13,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c20dade-6853-4500-9dcd-aa988788dca2/dqc_reference
[2024-01-24 10:57:14,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,647] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ad77dcf-1d8c-493b-bfd2-182abeee2381/GCF_004799685.1_ASM479968v1_genomic.fna.gz | prodigal -d GCF_004799685.1_ASM479968v1_genomic.fna/cds.fna -a GCF_004799685.1_ASM479968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:32,031] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:32,032] [INFO] Task started: HMMsearch
[2024-01-24 10:57:32,032] [INFO] Running command: hmmsearch --tblout GCF_004799685.1_ASM479968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c20dade-6853-4500-9dcd-aa988788dca2/dqc_reference/reference_markers.hmm GCF_004799685.1_ASM479968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:32,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:32,362] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8ad77dcf-1d8c-493b-bfd2-182abeee2381/GCF_004799685.1_ASM479968v1_genomic.fna.gz]
[2024-01-24 10:57:32,400] [INFO] Query marker FASTA was written to GCF_004799685.1_ASM479968v1_genomic.fna/markers.fasta
[2024-01-24 10:57:32,401] [INFO] Task started: Blastn
[2024-01-24 10:57:32,401] [INFO] Running command: blastn -query GCF_004799685.1_ASM479968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c20dade-6853-4500-9dcd-aa988788dca2/dqc_reference/reference_markers.fasta -out GCF_004799685.1_ASM479968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:33,008] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:33,012] [INFO] Selected 6 target genomes.
[2024-01-24 10:57:33,012] [INFO] Target genome list was writen to GCF_004799685.1_ASM479968v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:33,020] [INFO] Task started: fastANI
[2024-01-24 10:57:33,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad77dcf-1d8c-493b-bfd2-182abeee2381/GCF_004799685.1_ASM479968v1_genomic.fna.gz --refList GCF_004799685.1_ASM479968v1_genomic.fna/target_genomes.txt --output GCF_004799685.1_ASM479968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:39,880] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:39,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c20dade-6853-4500-9dcd-aa988788dca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:39,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c20dade-6853-4500-9dcd-aa988788dca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:39,887] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:39,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:39,887] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Halobellus limi	strain=CGMCC 1.10331	GCA_004799685.1	699433	699433	type	True	100.0	1248	1248	95	conclusive
Halobellus limi	strain=CGMCC 1.10331	GCA_900108165.1	699433	699433	type	True	99.9851	1239	1248	95	conclusive
Halobellus rarus	strain=YC21	GCA_024494595.1	1126237	1126237	type	True	90.4929	896	1248	95	below_threshold
Halobellus litoreus	strain=GX31	GCA_024464595.1	755310	755310	type	True	89.4294	927	1248	95	below_threshold
Halobellus rufus	strain=CBA1103	GCA_000739575.1	1448860	1448860	type	True	85.9394	767	1248	95	below_threshold
Halobellus captivus	strain=ZY21	GCA_007655485.1	2592614	2592614	type	True	84.5389	769	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:39,889] [INFO] DFAST Taxonomy check result was written to GCF_004799685.1_ASM479968v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:39,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:39,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:39,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c20dade-6853-4500-9dcd-aa988788dca2/dqc_reference/checkm_data
[2024-01-24 10:57:39,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:39,941] [INFO] Task started: CheckM
[2024-01-24 10:57:39,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004799685.1_ASM479968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004799685.1_ASM479968v1_genomic.fna/checkm_input GCF_004799685.1_ASM479968v1_genomic.fna/checkm_result
[2024-01-24 10:58:28,114] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:28,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:28,134] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:28,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:28,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004799685.1_ASM479968v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:28,136] [INFO] Task started: Blastn
[2024-01-24 10:58:28,136] [INFO] Running command: blastn -query GCF_004799685.1_ASM479968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c20dade-6853-4500-9dcd-aa988788dca2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004799685.1_ASM479968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:28,678] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:28,682] [INFO] Selected 5 target genomes.
[2024-01-24 10:58:28,682] [INFO] Target genome list was writen to GCF_004799685.1_ASM479968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:28,687] [INFO] Task started: fastANI
[2024-01-24 10:58:28,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad77dcf-1d8c-493b-bfd2-182abeee2381/GCF_004799685.1_ASM479968v1_genomic.fna.gz --refList GCF_004799685.1_ASM479968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004799685.1_ASM479968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:33,789] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:33,794] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:33,794] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004799685.1	s__Halobellus limi	100.0	1248	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000739575.1	s__Halobellus rufus	85.9427	767	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655485.1	s__Halobellus captivus	84.57	767	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665925.1	s__Halobellus sp003665925	84.1754	732	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665935.1	s__Halobellus sp003665935	83.8683	669	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:33,796] [INFO] GTDB search result was written to GCF_004799685.1_ASM479968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:33,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:33,802] [INFO] DFAST_QC result json was written to GCF_004799685.1_ASM479968v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:33,802] [INFO] DFAST_QC completed!
[2024-01-24 10:58:33,802] [INFO] Total running time: 0h1m21s